BatchJobs v1.8

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Batch Computing with R

Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.

Functions in BatchJobs

Name Description
batchExpandGrid Map function over all combinations.
cfReadBrewTemplate Cluster functions helper: Read in your brew template file.
callFunctionOnSSHWorkers Call an arbitrary function on specified SSH workers.
makeClusterFunctionsSSH Create an SSH cluster to execute jobs.
getResources Function to get job resources in job function.
makeRegistry Construct a registry object.
makeJob Creates a job description.
getSSHWorkersInfo Print and return R installation and other information for SSH workers.
showLog Display the contents of a log file.
makeClusterFunctionsTorque Create cluster functions for torque-based systems.
cfBrewTemplate Cluster functions helper: Brew your template into a job description file.
debugMulticore Helper function to debug multicore mode.
showStatus Retrieve or show status information about jobs.
addRegistrySourceDirs Add source dirs to registry.
cfHandleUnknownSubmitError Cluster functions helper: Handle an unknown error during job submission.
sweepRegistry Sweep obsolete files from the file system.
filterResults Find all results where a specific condition is true.
batchQuery Manually query the BatchJobs database
batchReduce Reduces via a binary function over a list adding jobs to a registry.
addRegistrySourceFiles Add source files to registry.
findJobs Finds ids of jobs that match a query.
debugSSH Helper function to debug SSH mode.
cfKillBatchJob Cluster functions helper: Kill a batch job via OS command
batchUnexport Unload exported R objects.
findDone Find jobs depending on computional state.
getErrorMessages Get error messages of jobs.
checkIds Check job ids.
configuration BatchJobs configuration.
getConfig Returns a list of BatchJobs configuration settings
syncRegistry Syncronize staged queries into the registry.
getJobLocation Get the physical location of job files on the hard disk.
copyRequiredJobFiles ONLY FOR INTERNAL USAGE.
getJobIds Get ids of jobs in registry.
getJobParamDf Retrieve Job Parameters.
getJobNr Get number of jobs in registry.
getJobInfo Get computational information of jobs.
makeClusterFunctionsSLURM Create cluster functions for SLURM-based systems.
makeClusterFunctionsSGE Create cluster functions for Sun Grid Engine systems.
reduceResults Reduce results from result directory.
getJobResources Function to get the resources that were submitted for some jobs.
removeRegistry Remove a registry object.
loadExports Load exported R data objects.
sanitizePath Sanitize a path
killJobs Kill some jobs on the batch system.
loadConfig Load a specific configuration file.
getJobs Get jobs from registry by id.
getLogFiles Get log file paths for jobs.
dbGetJobs ONLY FOR INTERNAL USAGE.
dbCreateJobDefTable ONLY FOR INTERNAL USAGE.
loadRegistry Load a previously saved registry.
removeRegistrySourceFiles Remove source files from registry.
loadResult Loads a specific result file.
setRegistryPackages Set packages for a registry.
resetJobs Reset computational state of jobs.
showClusterStatus Show information about available computational resources on cluster.
makeClusterFunctionsLSF Create cluster functions for LSF systems.
testJob Tests a job by running it with Rscript in a new process.
loadResults Loads result files for id vector.
makeClusterFunctions Create a ClusterFuntions object.
setConfig Set and overwrite configuration settings
makeClusterFunctionsLocal Create cluster functions for sequential execution on local host.
setJobFunction Sets the job function for already existing jobs.
updateRegistry ONLY FOR INTERNAL USAGE.
waitForJobs Wait for termination of jobs on the batch system.
setJobNames Set job names.
getJob Get job from registry by id.
makeClusterFunctionsInteractive Create cluster functions for sequential execution in same session.
grepLogs Grep log files for a pattern.
installPackagesOnSSHWorkers Install packages on SSH workers.
removeRegistryPackages Remove packages from registry.
makeClusterFunctionsMulticore Use multiple cores on local Linux machine to spawn parallel jobs.
removeRegistrySourceDirs Remove packages from registry.
makeClusterFunctionsOpenLava Create cluster functions for OpenLava systems.
makeSSHWorker Create SSH worker for SSH cluster functions.
makeSubmitJobResult Create a SubmitJobResult object.
submitJobs Submit jobs or chunks of jobs to batch system via cluster function.
sourceRegistryFiles Source registry files
batchMapResults Maps a function over the results of a registry by using batchMap.
batchExport Export R object to be available on the slaves.
BatchJobs The BatchJobs package
batchMap Maps a function over lists or vectors, adding jobs to a registry.
batchMapQuick Combination of makeRegistry, batchMap and submitJobs.
addRegistryPackages Add packages to registry.
applyJobFunction applyJobFunction ONLY FOR INTERNAL USAGE.
batchReduceResults Reduces results via a binary function and adds jobs for this to a registry.
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URL https://github.com/tudo-r/BatchJobs
BugReports https://github.com/tudo-r/BatchJobs/issues
MailingList batchjobs@googlegroups.com
License BSD_2_clause + file LICENSE
LazyData yes
ByteCompile yes
RoxygenNote 6.1.1
Encoding UTF-8
NeedsCompilation no
Packaged 2019-05-09 08:41:04 UTC; lang
Repository CRAN
Date/Publication 2019-05-14 22:00:16 UTC

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